I had a troubling experience the other day while submitting a paper. I was flagged for self-plagiarism. Turns out that according to this journal’s policies, the reuse of figures from a conference abstract in the full publication is not allowed. Just so we’re clear, I’ve put the outlines of both the conference abstract (4 page expanded abstract–think of it as a short paper, which is NOT peer reviewed) and the full publication below:

Conference abstract

Paper

AbstractIntro

Linear methodology

Synthetic Linear Example

Conclusions

AbstractIntro

Linear methodology

Synthetic Linear Example

Nonlinear methodology

Synthetic Nonlinear Example

Field Nonlinear Example

Conclusions

The linear synthetic example is identical between the two, and lots of the intro text and some of the linear methodology is the same. It is the nonlinear methodology that is the focus of the paper; the linear development is just required for a logical derivation of the nonlinear case. Though seemingly obtuse to me, I can understand the desire to not have identical blocks of text, and am more than happy to rewrite those–that’s 20 minutes of work. However, not being able to reuse the example is concerning to me. I want to make it clear I’m not particularly worried about this publication, but I’m worried about what this particular case represents.

Basically I have three options: (1) remove the offending example entirely, (2) reference the conference proceeding instead of showing the example, and (3) develop a different synthetic example.

(1) is obviously not an option; the example is there for a reason (the development of the nonlinear case requires the proof of the concept in the linear case). (3) can be done, but seems like a waste of time. (2) is a horrifying prospect.

These conference abstracts aren’t peer reviewed. The session chair looks them over, and basically gives them a go/no-go. Some conferences are a little more rigorous, but in all cases it is essentially a binary accept/don’t accept. I can tell you both as a past session chair and as a reviewer that the abstracts are not scrutinized like a journal article would be. Frankly a lot of garbage gets through–anyone who’s been to any conference will have encountered that. By not allowing the reproduction of any material from abstract to journal article, the organization is placing the abstracts on par with journal articles. In my particular case, the AE actually said the material is already published, you can’t publish it again.

Now here’s the issue. Authors are being encouraged to simply cite their abstracts, which means that a block of their manuscript, maybe a critical point, will never undergo peer review. What this demonstrates is that reviewers are and will increasingly be under an additional burden to review any abstracts that the paper cites. And reviewers are busy people–they’re chosen by the associate editor because they’re experts; they’re not going to take that kind of time. The potential for abuse of the system by less than scrupulous authors is extreme. Even if an author is well-intentioned, a subtle error may be propagated through multiple journal articles.

Let us assume that no abuse (intentional or otherwise) of the system occurs. This policy still completely disincentivizes presentation at the conference. Because abstracts are not peer reviewed, they are invisible to academic and research institutions when considering advancement or tenure. They simply don’t count. They mean nothing. So while the presented work might be extremely valuable and cited hundreds of times, that gives no personal boost to your career. Moreover, these extended abstracts are not a trivial effort, especially given the premium this organization seems to place on them. Why would I go to the time and expense of preparing a short paper that will not benefit my career whatsoever when I can just take the time to prepare the full journal article? Sure, there are lots of benefits to presenting your work at a conference, but under this policy I don’t think it’s worth it. Taking that a step further, why would I continue to be a member of the organization if I’m not going to attend the conferences (since as a government employee it’s nearly impossible to travel if not presenting)? I’ve been a member of this organization for over 10 years, and I’m thinking of not renewing this year.

Self-plagiarizing is an issue within our community (a certain colleague refers to it as auto-erotic referencing). We all know that scientist who references his own papers dozens of times in each subsequent paper. However, I believe this to be a completely separate situation. I am happy that they take plagiarism as seriously as they do, and I’m delighted that their automated software nailed the submission. However, I think this is going too far and frankly see this policy as damaging to the organization as a whole. I hope they reconsider their policy.

I got a request to post details of our all-grain setup here. Unfortunately, it’s in another state, but I’m slowly rebuilding it–better.

Our system was a recirculating mash system (RMS) with fairly precise temperature control. The temperatures were controlled via a python code written by Trevor, which took input from strategically placed thermocouples and activated hot water heater elements as necessary. This allowed us to very easily control our mash temperatures, giving us an enormous amount of control on the final flavors.

All-grain brew tutorial
For those who are familiar with all grain brewing, skip this section. For the rest, here is a short and basic tutorial on all grain brewing. All grain means you get all of your fermentable sugars from grain, rather than adding some kind of malt extract.

Basically, you need to ‘mash’ your grain at a particular temperature and water content to optimally activate the enzymes that convert starch into fermentable sugar. By controlling the temperature, you can activate/deactivate (or even denature) particular groups of enzymes (alpha amylase being the primary one) to control how ‘sweet’ or ‘dry’ the beer will be. Temperature and timing is everything. Generally the mash is somewhere in the neighborhood of 150-160 degrees Farenheit.

At the end of the mash, the ‘wort’ (pronounced wert, like Bert in Bert and Ernie) is sent to the boil, where it is heated to boiling and hops are added. After some period of time (generally something like an hour), the wort is cooled, transferred to a sterile vessel, yeast is added, and the yeasties are left to work their magic.

Our system produced between 10 and 12 gallons of beer per batch, requiring about 25 pounds of grain and a half pound of hops (depending on the recipe, of course). Our hot liquor tank (which just holds hot water), consisted of a keg with the top cut off, a valve installed in the bottom, and a thermocouple installed on the inside which controlled a stainless steel hot water heater element installed in the bottom (Figure 1, element 1).

A pump (4) would drain the tank into the Mash Tun (that which holds the grain for the mash), which was also a keg with a false bottom and valve assembly installed (2). The hot water would flow through a heat-exchanger (5), which was a water-filled vessel (an old soda keg) controlled by another hot water heater element. The water or wort being pumped through was contained in a coil, and the temperature of the exiting liquid was read by a thermocouple which controlled the temperature of the heat exchanger. The wort would be continuously circulated, keeping the temperature constant, for at whatever temperature and whatever time the recipe called for.

At the end of the mash, the wort would be pumped into the boil (3), which was another keg heated by a turkey fryer propane burner (6). This burner could go to 11, so we had to make sure to bring the wort to a boil slowly to avoid pyrolysis or caramelization. At this point we added hops and whatnot, and during the boil would replace the hot water in the heat exchanger with cold water.

At the end of the boil, we would run some boiling wort through the system to make sure it all was sanitary, then cool the boil using the heat exchanger. Pump into carboys, pitch the yeast, and go home.

The python interface controlling the temperatures was key. We could make a very clear beer just spot on whatever recipe we designed. Aside from having to take it apart to clean it every time, it was so much easier than stovetop.

On day 2, I made a pumpkin beer, while on day 3 I made a Dunkelweizen. The pumpkin beer was a bit of a failure, but I’ll describe my process here anyway. The Dunkel was a store-provided partial-mash recipe (fairly uninteresting) so I won’t post it here. Day 4 would have been an off-Friday anyway, which is good because I spent the weekend in Estes Park at a wedding. Which means that on Monday, I still didn’t even want to THINK about beer. As an aside, it’s quite sobering to see the destruction in and around Estes Park from the floods.

For the pumpkin beer, I took a mild Amber recipe, kicked the hops down a notch (basically didn’t use the finishing hops), and then added a whole pumpkin + spice + brown sugar + lactose (for non-fermentable sugar) puree into the end of the boil, just to sterilize it. It smells good, and the fermentation practically exploded, but the OG was pretty low and I’m afraid filtering might be necessary. I don’t think cold-crashing secondary will do the trick. But we’ll see.

I know, I’m way behind–today is for catch-up. Government shutdown, day 1.

A friend of mine and I built a recirculating mash system (RMS) for all-grain brewing. 10-12 gallon batches, wonderful results. Being geeks, the temperatures were all computer controlled. Unfortunately, he moved to Salt Lake City, and took the system (dubbed ‘valvezilla’) with him. I’m currently rebuilding the system, with hopefully actuated valves so the entire operation can be computer controlled.

Anyway, this means that I have to go back to partial-mashes. It’s been a long time, so we’ll see how my recipes turn out. Anyway, here’s my day one recipe–a Marzen, along with batch notes. The temperatures are idealized, and I definitely was not able to nail the temps on the stovetop.

This is a darker color but still fairly light-bodied American Marzen style.

I did a ‘stepped’ (again, stovetop so take with a grain of salt) mash, shooting for 152F for 30 min and 160 for 30 min. Bring to boil, add DME, etc etc. The intent was to put 1 oz of each hops in for 60 min, then the rest in at 15 min, but due to logistics with my hop bags, T was bittering and H was ‘aroma’. Cooled, pitched lager yeast, let fermentation start (a few hours), then into the fridge for 3 weeks of lagering before racking into secondary, and probably giving it another 3 weeks.

A Marzen (Ersten Marzen) was the first beer I ever brewed, and ranks among my favorite styles (both German and American styles). I will say that my palette enjoys a maltier Marzen than is typical (e.g. a Sam Adams Octoberfest), but they’re all delicious.

Those reading likely are aware that I am a research scientist with the US Geological Survey. That is, until Congress shut down the government; now I am furloughed along with 800,000 other Federal Employees. I am literally forbidden from working, even on a volunteer basis.

I’ve had several friends say something to the effect of ‘I wish I got a vacation.’ Well this isn’t a vacation. This is unpaid leave. What’s worse is that Congress has made a statement, and their statement boils down to: ‘our bickering is more important than the work you do for the people.’ I take great offense to this. I, and every other scientist I work with, take great pride in what we do. And right now that doesn’t feel very appreciated.

Like my Dad used to say, when life gives you lemons, make beer. Well it wasn’t exactly like that but close enough. I am therefore brewing beer every day I am furloughed. For those interested I will document my brews here.

One of my first posts on this blog was in recognition of the heroic sacrifices made by the Apollo 1, Challenger, and Columbia crews, as well as a handful of other astronauts who were killed in training missions. Today marks the 10 year anniversary of the Columbia tragedy, where the shuttle broke up over North America on reentry.

I had just moved to Colorado from Dallas, and my Dad sent me this picture (he didn’t take it but I’m not sure where he got it, so I apologise for the lack of citation):

This was eerie enough, but hearing the transmission get cut off mid-word was even eerier. Let’s take a moment today to remember these astronauts–risking and giving their lives to advance human knowledge of the universe.

In a Nature Letter (and I’m sorry if that’s behind a paywall–I can’t tell from here), researchers at the European Bioinformatics Institute and Agilent Technologies introduced a method of encoding information onto DNA. The concept is not terribly new, but I appreciate their thoughtful approach to addressing many of the problems in DNA data storage.

To test their method, the researchers encoded the works of Shakespeare, an excerpt from MLK’s “I have a dream” speech, a photo of their lab, the famous Watson and Crick DNA paper (which I just love the tip of the hat to those that made this possible) and their encoding procedure (totaling about 3/4 of a MB) onto DNA, then shipped it to Germany from the USA, and decoded the information with a stated 100% recovery rate.

I really appreciate the work of these researchers, because they’ve moved beyond the ‘because we can’ and have given us very good practical reasons why one would want to store information on DNA. Among them is that DNA fragments will remain viable for thousands of years with a fairly modest storage scheme. In addition, encoding onto DNA ensures we will not forget how to decode the information–it is likely that as long as we don’t bomb ourselves back to the stone age we will continue to be able to read and write DNA (unlike some of my own data from graduate school). Also, the data density is on the order of 2 petabytes per gram (that’s 10^15 bytes or 1000 terabytes). They even compare the costs of DNA storage over magnetic tapes.

Their encoding scheme was interesting to me as well. From the paper, it is my understanding that repeated nucleotides tend to break. So rather than encoding information into a base-4 system, they encoded it into trinary and used the last nucleotide almost as a dummy (that’s a bit of a simplification). They have about a x4 redundancy in how they write the data, and other clever methods, like indexing nucleotides on the ends of the fragments.

It’s research like this that drives industry. I’m excited about the implications of this. Sure, this method isn’t for rapid storage and recovery, but (as the authors point out) for applications like CERN, who produce massive quantities of data, this is a boon. Imagine other applications: encoding literature, music, art, scientific advances, all onto a storage medium that can last for tens of thousands of years. I think the benefits of this research become clear.

Occasionally, I will have a conversation with someone regarding climate change. This is often with a coworker of my wife’s–she is an engineer, so she and her coworkers are generally quite intelligent people, but have zero background in any of the sciences that go with studying a changing climate. Usually these conversations are completely amicable, and amount to simply an exchange of facts, with a few qualified speculations thrown in.

One individual, however, refuted the existence of a changing climate. When presented with appropriate data, he stated that it was bunk (with no supporting data or reasons for his disregard of published data), and accused me of (and I quote) “drinking the kool-aid.” I presume this means he doesn’t trust my climate change data because I work for the US Geological Survey, and in his mind we have some agenda which relies on convincing the public there’s a changing climate. I should note that I was not proposing the causes of climate change, only the existence.

First of all, let me say that the USGS is a fact-finding organization only–we have no oversight or enforcement responsibilities, and therefore do not benefit at all whether or not climate change really exists.

Secondly, I’m personally offended when someone questions my scientific integrity. I may not be the best or most brilliant scientist in the world, but damnit I’m honest. That was the closest I’ve ever come to requesting that someone call me Dr. Kass, just to be, well frankly, a prick.

More to the point, however, I don’t understand how someone can simply reject data that does not agree with their personal, uninformed opinions. I know it’s an old argument, but it amazes me every time. I’m up for debating this if someone cares to present a rational case against climate change (in fact, I have had stimulating discussions like this in the past), but the moment you reject evidence in favour of…passion? religion? faith? denial? (I have no idea)…the conversation with me is over.

Given his actions, he is clearly an irrational person, and no amount of discussion, presentation, or debate will affect his viewpoint. I SHOULD let it go, but this was probably over a year ago and it still bothers me.

Well, at least one thing I CAN do in this regard is to pass along public climate change data when I get it. So here goes.

I received an email this morning from the Cryolist that I thought I’d share. It contained a link to this year’s glacier mass balance data from the World Glacier Monitoring Service at the University of Zurich, which shows how much mass loss (or gain, in a few cases) a series of approximately 100 glaciers experienced over the past year, and incorporates that data into the historical records. All of the data I’m about to discuss is available through their website at the link above.

Mass balance data is reported in a bit of an odd unit – metres of water equivalent (m w.e.), which roughly can be described as the average thickness the glacier lost or gained. There are a variety of ways this can be measured, but I won’t go into that here.

Below is an overview of their preliminary 2010/2011 data. I took this table directly from their website.

Table 1: Overview on mass balance data 2010/11. Statistics are given for all reported glaciers (ALL) and for the available ‘reference’ glaciers with continuous long-term observation series (REF).

.

2010/11

.

ALL

REF

Mean annual mass balance (mm w.e.)

-755

-1046

Minimum value (mm w.e.)

-4153

-4153

Maximum value (mm w.e.)

1640

1210

Standard deviation (mm w.e.)

1103

976

Number of positive/reported balances

25/108

3/32

This is not a very pleasant set of numbers. We’ve lost, on average, roughly a metre off the world’s glaciers in the past year. A sobering chart, again from their website, is given below:

Of course, these data only go back to 1980, and we know that there are long-period temperature cycles in the Earth that the temporal extent cannot show. However, these are still scary numbers in the short term. I would rather take my children to see glaciers rather than just show them pictures from a book.

I think it’s important we as a society keep up with these data as they are released. No one dataset is definitive, or shows a long term view, but they are valuable nonetheless. I will continue to post data such as these as they come across my desk, but if you want to get the same notifications I do, check out cryolist.org.

NASA and the ESA announced a few days ago the discovery of an asteroid belt around Vega. I find this exciting, for several reasons, not the least of which is that we can all go outside and find Vega quite easily in the night sky–in fact it’s one of the brightest (in the summer, it’s part of the Summer Triangle which includes Deneb and Altair, and sits in the constellation Lyra).

What is even more important, is that the presence of an asteroid belt suggests the presence of planets. With all the discoveries of Exoplanets these days from the Kepler Observatory and others, it’s tempting to say ‘so what?’ and move on. But, Vega is only about 600 million years old. We get to watch a young solar system continue to form and grow from only 25 light years away.

Solar system and Vega system comparison. Image credit: NASA/JPL-Caltech.

Vega is similar to another star, Fomalhaut, where in 2008 the Hubble Telescope directly imaged an exoplanet. The discovery wasn’t confirmed until late last year, due to the severe elliptical orbit (which may have been caused by the orbits of other planets). Fomalhaut is another star, roughly the same age and distance from us as Vega, that can be seen with the naked eye in the night sky (low in the fall and winter, in Pisces).

So even though we can’t see these planets with ground-based telescopes, I still like to turn mine to Vega and Fomalhaut now. I might just be looking at a point of light from my perspective, but I know that there are planets orbiting, and somehow it makes it a little more special.

For more information: http://www.jpl.nasa.gov/news/news.php?release=2013-012

Oh, and just for funsies: as of 0816 MST on the 10th of January, 2013, Voyager 1 is 18,501,453,800 kilometers from Earth. Light from the sun takes 17 hours, 8 minutes, and 38 seconds to reach her.